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atacproc

ATAC-seq processing pipeline

avesim

AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.

awesome-guidelines

A curated list of high quality coding style conventions and standards.

cheatsheets

RStudio Cheat Sheets

chipline

ChIP-seq analysis pipeline

dge_workshop

efficientr

Efficient R programming: a book

fastbook

Draft of the fastai book

flowincubator

Routines that don't belong to the core flow packages yet.

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hic_tools

A collection of tools for Hi-C data analysis

hicnv

HiCnv is used to call copy number variations and breakpoints from Hi-C data

hictrans

HiCtrans is a pipeline to call translocations from Hi-C data

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

karyoploter

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

lji_rna_seq_pipeline_v2

Snakemake based RNA-Seq QC pipeline for cloud/cluster implementation

mess

Miscellaneous Esoteric Statistical Scripts - an R package

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

purrr

Make your pure R function purrr with functional programming

r4ds

R for data science

rcpp

Seamless R and C++ Integration

rcppexamples

Examples of using Rcpp to interface R and C++

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

singlecellworkshop

upsetr

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..